A method of starting up and shutting down a microchannel process is provided. Included are the steps of providing a first multi-planar process unit, preferably adapted to process an endothermic reaction, a second multi-planar process unit, preferably adapted to process an exothermic reaction, providing a containment vessel, the containment vessel containing at least a portion of the first, and preferably the second, process unit. In startup, the microchannel process is first checked for pressure integrity by pressurizing and checking the important components of the process for leaks. Subsequently, the process units are heated by introducing a dilute low-thermal energy density material, preferably to the second process unit, followed by the introduction of a dilute high-thermal energy density material, and adjusting the proportion of high-thermal energy density material as required. In shutdown, a purge material from the containment vessel is introduced into the first, and preferably the second, process unit.